Provided by: libbio-perl-perl_1.7.6-3_all bug


       Bio::Tools::Signalp::ExtendedSignalp - enhanced parser for Signalp output


        use Bio::Tools::Signalp::ExtendedSignalp;
        my $params = [qw(maxC maxY maxS meanS D)];
        my $parser = new Bio::Tools::Signalp::ExtendedSignalp(
                                                              -fh      => $filehandle
                                                              -factors => $params

        while( my $sp_feat = $parser->next_feature ) {
              #do something
              push @sp_feat, $sp_feat;


       # Please direct questions and support issues to

       Parser module for Signalp.

       Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally
       written by Marc Sohrmann (ms2 a Written in BioPipe by Balamurugan Kumarasamy
       (savikalpa a Cared for by the Fugu Informatics team (

       You may distribute this module under the same terms as perl itself

       Compared to the original SignalP, this method allow the user to filter results out based
       on maxC maxY maxS meanS and D factor cutoff for the Neural Network (NN) method only. The
       HMM method does not give any filters with 'YES' or 'NO' as result.

       The user must be aware that the filters can only by applied on NN method.  Also, to ensure
       the compatibility with original Signalp parsing module, the user must know that by
       default, if filters are empty, max Y and mean S filters are automatically used to filter

       If the used gives a list, then the parser will only report protein having 'YES' for each

       This module supports parsing for full, summary and short output form signalp.  Actually,
       full and summary are equivalent in terms of filtering results.


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        Based on the Bio::Tools::Signalp module
        Emmanuel Quevillon <>


        The rest of the documentation details each of the object methods.
        Internal methods are usually preceded with a _

        Title   : new
        Usage   : my $obj = new Bio::Tools::Signalp::ExtendedSignalp();
        Function: Builds a new Bio::Tools::Signalp::ExtendedSignalp object
        Returns : Bio::Tools::Signalp::ExtendedSignalp
        Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

        Title   : next_feature
        Usage   : my $feat = $signalp->next_feature
        Function: Get the next result feature from parser data
        Returns : Bio::SeqFeature::Generic
        Args    : none

        Title   : _filterok
        Usage   : my $feat = $signalp->_filterok
        Function: Check if the factors required by the user are all ok.
        Returns : 1/0
        Args    : hash reference

        Title   : factors
        Usage   : my $feat = $signalp->factors
        Function: Get/Set the filters required from the user
        Returns : hash
        Args    : array reference

        Title   : _parsed
        Usage   : obj->_parsed()
        Function: Get/Set if the result is parsed or not
        Returns : 1/0 scalar
        Args    : On set 1

        Title   : _parse
        Usage   : obj->_parse
        Function: Parse the SignalP result
        Returns :
        Args    :

        Title   : _parse_summary_format
        Usage   : $self->_parse_summary_format
        Function: Method to parse summary/full format from signalp output
                  It automatically fills filtered features.
        Returns :
        Args    :

        Title   : _parse_nn_result
        Usage   : obj->_parse_nn_result
        Function: Parses the Neuronal Network (NN) part of the result
        Returns : Hash reference
        Args    :

        Title   : _parse_hmm_result
        Usage   : obj->_parse_hmm_result
        Function: Parses the Hiden Markov Model (HMM) part of the result
        Returns : Hash reference
        Args    :

        Title   : _parse_short_format
        Usage   : $self->_parse_short_format
        Function: Method to parse short format from signalp output
                  It automatically fills filtered features.
        Returns :
        Args    :

        Title   : create_feature
        Usage   : obj->create_feature(\%feature)
        Function: Internal(not to be used directly)
        Returns :
        Args    :

        Title   : seqname
        Usage   : obj->seqname($name)
        Function: Internal(not to be used directly)
        Returns :
        Args    :